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Reposted by Hani Goodarzi

pauldatlinger.bsky.social @pauldatlinger.bsky.social · 14d

#CELLFIE for CAR T screening—a new mRNA-based platform for screening primary cells. CAR + gRNA library are delivered by lentivirus, CRISPR modifiers as electroporated mRNA. That’s more flexible and effective than existing T cell screening methods. (1/7)

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Reposted by Hani Goodarzi

Andrei Goga @andreigoga.bsky.social · Aug 20

New work from stellar scientists Jeremy Williams and Roman Camarda. Many contributors including the amazing Zena Werb and Atul Butte

Work explores how breast cancer cells interact directly with adipocytes via gap junctions, leading to lipid release.
@ctbatucsf.bsky.social @ucsfcancer.bsky.social

Tumor cell-adipocyte gap junctions activate lipolysis and contribute to breast tumorigenesis

Nature Communications - Breast cancer cells interact with neighbouring adipocytes, but the mechanisms are not fully understood. Here, the authors show that triple-negative breast cancer (TNBC)...

www.nature.com

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Reposted by Hani Goodarzi

Ryan Flynn @raflynn5.bsky.social · Aug 6

RNA N-glycosylation enables immune evasion and homeostatic efferocytosis by chemically caging acp3U. Excited to report this work lead by Vinnie @vinnieviruses.bsky.social and in collaboration with @vijayrathinam.bsky.social in @nature.com www.nature.com/articles/s41...

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Reposted by Hani Goodarzi

Rita Strack @ritastrack.bsky.social · Jul 30

My colleagues at Nature Biomedical Engineering @natbiomedeng.nature.com are hiring an associate or senior editor. Ideal applicant will have expertise in immunology, immunotherapy, or immuno-oncology.

Please feel to ask me questions!

springernature.wd3.myworkdayjobs.com/SpringerNatu...

Associate or Senior Editor, Nature Biomedical Engineering

Job Title: Associate or Senior Editor, Nature Biomedical Engineering Organization: Nature Portfolio Location: New York, Jersey City, Shanghai or Beijing – Hybrid Working Closing date: August 20, 2025 ...

springernature.wd3.myworkdayjobs.com

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Hani Goodarzi @genophoria.bsky.social · Jul 24

Go @exai.bio! Looking forward to working with Mike as our incoming CEO and our amazing board members.

exai bio @exai.bio · Jul 23

We’re excited to welcome Michael Nall as CEO and Board Director and new Board Directors - Steve Kafka, PhD, of S32, Dusan Perovic of Two Sigma Ventures and Emir Sandhu, MD, of Blue Venture Fund. Their leadership will be invaluable as we advance our RNA & AI liquid biopsy platform.

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Reposted by Hani Goodarzi

Fusion Conferences @fusionconf.bsky.social · Jul 17

Are you currently in the ERE related field & want to find new collaborative opportunities? Join our Chairs @chiappinellilab.bsky.social, @shenhui1986.bsky.social, Ting & Tao at #EREHD25 this Nov!
🎙️Talk Submission extended to 03 Sept
💰Final few $500 grants remaining
Don't Miss out! bit.ly/4eRq9Mp

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Hani Goodarzi @genophoria.bsky.social · Jun 26

Congratulations... amazing!

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Reposted by Hani Goodarzi

Homa Majd @homamajd.bsky.social · Jun 25

Our ENS is vital to gut-brain health. When it breaks down, so does health. Treatments? Almost none.
Access to functional human enteric neurons at scale powers disease modeling and therapeutic discovery. Grateful to everyone who made this possible. www.nature.com/articles/s41...

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Hani Goodarzi @genophoria.bsky.social · Jun 14

Oh no! I am devastated!

euanashley @euanashley.bsky.social · Jun 14

Atul Butte died yesterday.
The world lost a giant.
A big bear of a man.
With a huge smile.
With love for everyone.
With energy that could power a room.
I loved everything about Atul.
I loved how he was always happy.
I loved how excited he was about science and helping people.

Reposted by Hani Goodarzi

Faraz Mardakheh @mardakheh.bsky.social · Jun 9

Check out this amazing work from @genophoria.bsky.social’s lab, revealing a novel post-transcriptional tumour suppressive programme in breast cancer 👇👇

Hani Goodarzi @genophoria.bsky.social · Jun 9

Been going back and forth on whether it makes sense to post science in the midst of all that is happening. But here it goes with a couple of days of delay:
www.biorxiv.org/content/10.1...

Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer

Heterogeneity in cancer gene expression is typically linked to genetic and epigenetic alterations, yet post-transcriptional regulation likely influences these patterns as well. However, the quantitati...

www.biorxiv.org

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Hani Goodarzi @genophoria.bsky.social · Jun 9

We would especially like to thank all of our colleagues who collaborated with us on this, including @balynzaro.bsky.social and Albertas Navickas, for their contributions to this work. And our funders, including @arcinstitute.org.

Hani Goodarzi @genophoria.bsky.social · Jun 9

Finally, we used double-knockdown for in vivo lung colonization assays to confirm the expected epistatic interaction between RBMS3 and TXNIP.

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Hani Goodarzi @genophoria.bsky.social · Jun 9

We confirmed that TXNIP is correlated with RBMS3, and similarly its expression is associated with better outcomes. Then we looked at TXNIP expression in a cohort of 96 breast cancer samples in-house, stratified by stage, that confirmed reduced expression as disease progresses.

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Hani Goodarzi @genophoria.bsky.social · Jun 9

To figure out which, if any, of the targets of RBMS3 that we identified are responsible for this phenotype, we performed an in vivo CRISPR screen. Among the targets tested, we found that silencing TXNIP increases metastatic lung colonization.

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Hani Goodarzi @genophoria.bsky.social · Jun 9

To turn this clinical association into causation, we took advantage of metastasis assays in xenografted mice. We showed that silencing and over-expressing RBMS3 modulates metastasis in vivo in two independent models.

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Hani Goodarzi @genophoria.bsky.social · Jun 9

Interestingly, this association was most notable in the basal and Claudin-low subtypes of breast cancer, which are known to be aggressive subtypes.

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Hani Goodarzi @genophoria.bsky.social · Jun 9

We consistently observed that reduced expression of RBMS3 is associated with poor clinical outcomes in breast cancer patients, in multiple datasets.

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Hani Goodarzi @genophoria.bsky.social · Jun 9

To gain insight into the functional consequences and phenotypic effects of this regulon, we looked at pathways and complexes that may be enriched among the RBMS3 target. We saw a significant enrichment for TGFb and VEGF signaling that are associated with metastatic progression in breast cancer.

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Hani Goodarzi @genophoria.bsky.social · Jun 9

Finally, we demonstrated the requirement and sufficiency of RBMS3 binding sites for this RBSM3-mediated transcript stabilization. We cloned binding sites from 13 high confidence mRNA targets into a reporter assay, which showed RBMS3-dependent increase in reporter expression.

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Hani Goodarzi @genophoria.bsky.social · Jun 9

Replacing AUA-carrying mRNAs with these empirical RBMS3 CLIP targets confirmed that RBMS3 direct binding drives transcript stabilization.

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Hani Goodarzi @genophoria.bsky.social · Jun 9

To show that this effect results from a direct interaction between RBMS3 and its target mRNAs, we performed CLIP-seq (UV crosslinking followed by immuno-precipitation and sequencing). We observed pervasive 3’UTR binding, and also a strong enrichment for the AUA element we had identified.

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Hani Goodarzi @genophoria.bsky.social · Jun 9

Silencing RBMS3, as expected, resulted in a significant decrease in the stability and expression of the mRNAs that contain AUA-elements in their 3’UTRs.

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Hani Goodarzi @genophoria.bsky.social · Jun 9

Among these, we chose RBMS3 for further characterization, simply because it was the highest ranking RBP for correlated expression with its putative regulon—identified based on the AUA cis-regulatory element, which was determined by analysis of GreyHound’s sequence importance scores.

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Hani Goodarzi @genophoria.bsky.social · Jun 9

Applying GreyHound to our breast cancer mRNA stability dataset, we uncovered a network of RBPs associated, and their cognate cis-regulatory elements, as a major determinant of variation in the RNA dynamics of breast cancer.

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Hani Goodarzi @genophoria.bsky.social · Jun 9

To help decipher the regulatory grammar of context-specific mRNA dynamics, we developed GreyHound: a multimodal deep-learning model that integrates RNA sequences and RNA-binding protein (RBP) expression to predict mRNA stability.

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